cBioPortal validation report

Study directory:
./generated_data/blca_tcga_gdc

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version 6.0.8

Validation status: Please check
Line Number Column Number Message Value Encountered
Debug Requesting info from portal at 'https://www.cbioportal.org'
Debug Requesting cancer-types from portal at 'https://www.cbioportal.org'
Debug Requesting genes from portal at 'https://www.cbioportal.org'
Debug Requesting genesets from portal at 'https://www.cbioportal.org'
Debug Requesting genesets_version from portal at 'https://www.cbioportal.org'
Debug Requesting gene-panels from portal at 'https://www.cbioportal.org'
Debug Retrieving chromosome lengths from '/Users/jko/Code/nci-crdc-pipeline/scripts/importer/chromosome_sizes.json'
Debug Validating case lists
Info Validation of case list folder complete
Info Validation complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 272 OS_MONTHS is not specified for deceased patient. Patient will be excluded from survival curve and month of death will not be shown on patient view timeline. <none>
Info Validation of file complete
Info Read 417 lines. Lines with warning: 1. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 418 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 86, 177, 178… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1768 values
Info Validation of file complete
Info Read 38322 lines. Lines with warning: 1768. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 12140, 67898, 111610… Segment is zero bases wide and will not be loaded 10131410-10131410, 134773134-134773134, 32425075-32425075 See all 4 values
Info Validation of file complete
Info Read 162107 lines. Lines with warning: 4. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 3 Including the SWISSPROT column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view
Info 6, 8, 15… Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA] Silent, Intron, 5'UTR… See all 31952 values
Warning 344, 724, 1379… Entrez gene id exists, but gene symbol specified is not known to the cBioPortal instance. The gene symbol will be ignored. Might be wrong mapping, new or deprecated gene symbol. TTC30A, UHRF1BP1, TRIM75P… See all 287 values
Warning 8034, 10430, 12203… Gene symbol not known to the cBioPortal instance. This record will not be loaded. FAM155A, KIAA1841, FAM160B1… See all 30 values
Warning 55232, 57939, 102711 No Amino_Acid_Change or HGVSp_Short value. This mutation record will get a generic "MUTATED" flag
Info Validation of file complete
Info Read 116687 lines. Lines with warning: 321. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 413 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 1307 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Warning Unrecognized field in meta file short_name
Info Validation of meta file complete
Info Setting reference genome to human (GRCh38, hg38)
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete

Legend

Click on a filename below to see a table of messages about the data in the file. The colors in the tables have the following meanings:

Error Error: cBioPortal will not know how to load this, please revise or remove
Warning Warning: possible cause of confusion, please check whether this is intended
Info Info: this looks good, no action required
Debug Verbose output: details on the progress of the validation script